Starting phenix.real_space_refine on Sun Sep 13 17:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zb4_11144/09_2026/6zb4_11144.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15856 2.51 5 N 4094 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24841 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8056 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 47, 'TRANS': 987} Chain breaks: 11 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8189 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 1002} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8158 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 999} Chain breaks: 11 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.91, per 1000 atoms: 0.20 Number of scatterers: 24841 At special positions: 0 Unit cell: (143.85, 151.2, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4777 8.00 N 4094 7.00 C 15856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM24659 O5 NAG B1309 .*. O " rejected from bonding due to valence issues. Atom "HETATM24443 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2102 " - " ASN A 714 " " NAG A2104 " - " ASN A 343 " " NAG B1309 " - " ASN B 234 " " NAG C1403 " - " ASN C 616 " " NAG C1406 " - " ASN C 234 " " NAG D 1 " - " ASN C 714 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 50 sheets defined 23.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.525A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.754A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.529A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.031A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.501A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 744 through 751 removed outlier: 3.943A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.599A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 833 through 838 removed outlier: 3.748A pdb=" N CYS C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.924A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 883 through 887' Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.693A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.516A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 1029 removed outlier: 3.838A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1015 " --> pdb=" O ARG C1011 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.018A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.593A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.967A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.673A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 750 removed outlier: 3.637A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.850A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.756A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 916 through 936 Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.439A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.628A pdb=" N ARG B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.987A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.019A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.657A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.906A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.562A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.772A pdb=" N ALA A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.771A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 937 removed outlier: 4.121A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.302A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.706A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.250A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.072A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.123A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.309A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.561A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.525A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.245A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.384A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 708 through 710 removed outlier: 3.907A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.592A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AB6, first strand: chain 'C' and resid 1083 through 1086 removed outlier: 4.105A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.541A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.643A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.884A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.749A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 230 removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.707A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.369A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 710 Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.577A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD4, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1122 removed outlier: 4.849A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 4.644A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AD8, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.172A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 65 through 66 removed outlier: 5.957A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.926A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.318A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.571A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.509A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N THR A 693 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF2, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.625A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF4, first strand: chain 'A' and resid 1078 through 1079 removed outlier: 4.202A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1091 through 1094 863 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4043 1.31 - 1.44: 7056 1.44 - 1.57: 14142 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25379 Sorted by residual: bond pdb=" C7 NAG B1306 " pdb=" N2 NAG B1306 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C7 NAG B1302 " pdb=" N2 NAG B1302 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1307 " pdb=" N2 NAG B1307 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1303 " pdb=" N2 NAG B1303 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C7 NAG C1401 " pdb=" N2 NAG C1401 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 25374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 33417 1.72 - 3.43: 902 3.43 - 5.15: 141 5.15 - 6.87: 22 6.87 - 8.59: 1 Bond angle restraints: 34483 Sorted by residual: angle pdb=" N ILE B 847 " pdb=" CA ILE B 847 " pdb=" C ILE B 847 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N MET C1047 " pdb=" CA MET C1047 " pdb=" C MET C1047 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.76e+01 angle pdb=" N ALA C 703 " pdb=" CA ALA C 703 " pdb=" C ALA C 703 " ideal model delta sigma weight residual 110.97 115.07 -4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA TYR B 37 " pdb=" CB TYR B 37 " pdb=" CG TYR B 37 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N GLY C 697 " pdb=" CA GLY C 697 " pdb=" C GLY C 697 " ideal model delta sigma weight residual 113.18 121.77 -8.59 2.37e+00 1.78e-01 1.31e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13078 17.88 - 35.76: 1352 35.76 - 53.64: 286 53.64 - 71.52: 86 71.52 - 89.40: 28 Dihedral angle restraints: 14830 sinusoidal: 5742 harmonic: 9088 Sorted by residual: dihedral pdb=" CA ARG C1088 " pdb=" C ARG C1088 " pdb=" N GLU C1089 " pdb=" CA GLU C1089 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP A 88 " pdb=" C ASP A 88 " pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 753 " pdb=" C TYR A 753 " pdb=" N GLY A 754 " pdb=" CA GLY A 754 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 14827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 3970 0.258 - 0.516: 2 0.516 - 0.773: 1 0.773 - 1.031: 0 1.031 - 1.289: 1 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 714 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.15e+00 ... (remaining 3971 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.495 2.00e-02 2.50e+03 5.08e-01 3.23e+03 pdb=" CG ASN B 234 " -0.178 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.796 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.303 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C1402 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.435 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.299 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C7 NAG B1304 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.026 2.00e-02 2.50e+03 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 88 2.43 - 3.05: 15250 3.05 - 3.67: 31943 3.67 - 4.28: 51449 4.28 - 4.90: 90927 Nonbonded interactions: 189657 Sorted by model distance: nonbonded pdb=" O GLY A 339 " pdb=" OD1 ASN A 343 " model vdw 1.814 3.040 nonbonded pdb=" O ASN C 975 " pdb=" OG SER C 979 " model vdw 1.949 3.040 nonbonded pdb=" ND2 ASN C 343 " pdb=" O5 NAG C1401 " model vdw 1.966 3.120 nonbonded pdb=" O3 NAG B1310 " pdb=" O7 NAG B1310 " model vdw 2.051 3.040 nonbonded pdb=" O ASN A 975 " pdb=" OG SER A 979 " model vdw 2.072 3.040 ... (remaining 189652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 172 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 210 or resid 216 through 245 or resid 255 or resid 257 thro \ ugh 675 or resid 686 through 808 or resid 810 through 825 or resid 829 through 8 \ 40 or resid 845 through 931 or (resid 932 and (name N or name CA or name C or na \ me O or name CB )) or resid 933 through 2106)) selection = (chain 'B' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 172 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 210 or resid 216 through 255 or resid 257 through 675 or resid 686 through \ 807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or re \ sid 810 through 840 or resid 845 through 931 or (resid 932 and (name N or name C \ A or name C or name O or name CB )) or resid 933 through 936 or (resid 937 and ( \ name N or name CA or name C or name O or name CB )) or resid 941 through 1306)) selection = (chain 'C' and (resid 15 through 18 or resid 25 through 67 or resid 81 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 157 through 245 or resid 256 through 808 or resid 810 through 936 or (resid 9 \ 37 through 941 and (name N or name CA or name C or name O or name CB )) or resid \ 942 through 1406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.525 25417 Z= 0.345 Angle : 0.853 60.761 34566 Z= 0.402 Chirality : 0.051 1.289 3974 Planarity : 0.009 0.254 4419 Dihedral : 15.931 89.398 8885 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 3.84 % Allowed : 16.85 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.12), residues: 3063 helix: -1.95 (0.17), residues: 659 sheet: -1.71 (0.18), residues: 689 loop : -3.65 (0.11), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.020 0.001 TYR A 37 PHE 0.014 0.001 PHE C 592 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.30 (25379) covalent geometry : angle 0.69053 / 0.37 (34483) SS BOND : bond 0.00197 / 0.13 ( 31) SS BOND : angle 0.95622 / 0.60 ( 62) hydrogen bonds : bond 0.16710 / 10.14 ( 857) hydrogen bonds : angle 7.12674 / 4.98 ( 2313) link_BETA1-4 : bond 0.00379 / 0.20 ( 1) link_BETA1-4 : angle 2.49807 / 1.27 ( 3) link_NAG-ASN : bond 0.21942 / 11.02 ( 6) link_NAG-ASN : angle 21.87405 / 15.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 317 time to evaluate : 0.874 Fit side-chains REVERT: C 88 ASP cc_start: 0.7440 (t70) cc_final: 0.6991 (t0) REVERT: C 702 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (m) REVERT: C 773 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8438 (ttpt) REVERT: C 820 PHE cc_start: 0.7956 (t80) cc_final: 0.7280 (m-80) REVERT: C 983 LYS cc_start: 0.7815 (tptm) cc_final: 0.7487 (mmtm) REVERT: C 1078 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 1104 ARG cc_start: 0.7361 (mtt90) cc_final: 0.7105 (mpt180) REVERT: C 1112 ILE cc_start: 0.8548 (mt) cc_final: 0.8326 (mt) REVERT: B 115 GLN cc_start: 0.8737 (mt0) cc_final: 0.8449 (mt0) REVERT: B 661 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: B 675 GLN cc_start: 0.7150 (mm110) cc_final: 0.6891 (mm-40) REVERT: B 1088 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6986 (ptm-80) REVERT: B 1133 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7070 (p) REVERT: A 309 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: A 1070 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7257 (mmtp) outliers start: 104 outliers final: 60 residues processed: 398 average time/residue: 0.1552 time to fit residues: 99.9342 Evaluate side-chains 306 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN C 481 ASN C 487 ASN C 613 GLN C 752 GLN C 798 ASN C 952 ASN C1007 GLN C1045 HIS B 409 GLN B 487 ASN B 613 GLN B 655 HIS B 798 ASN B 952 ASN B1122 ASN A 606 ASN A 616 ASN A 898 GLN A 989 GLN A1068 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116960 restraints weight = 30381.342| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.74 r_work: 0.3058 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25417 Z= 0.138 Angle : 0.660 32.027 34566 Z= 0.332 Chirality : 0.048 0.697 3974 Planarity : 0.005 0.060 4419 Dihedral : 7.971 82.366 3484 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.55 % Allowed : 17.25 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.13), residues: 3063 helix: -0.40 (0.20), residues: 658 sheet: -0.95 (0.19), residues: 676 loop : -3.00 (0.12), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.031 0.002 TYR B 170 PHE 0.014 0.001 PHE B1118 TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (25379) covalent geometry : angle 0.61849 / 0.32 (34483) SS BOND : bond 0.00352 / 0.22 ( 31) SS BOND : angle 1.13672 / 0.72 ( 62) hydrogen bonds : bond 0.04695 / 3.09 ( 857) hydrogen bonds : angle 5.30629 / 3.74 ( 2313) link_BETA1-4 : bond 0.00977 / 0.51 ( 1) link_BETA1-4 : angle 2.60647 / 1.27 ( 3) link_NAG-ASN : bond 0.00761 / 0.55 ( 6) link_NAG-ASN : angle 9.95441 / 6.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 248 time to evaluate : 0.821 Fit side-chains REVERT: C 88 ASP cc_start: 0.8116 (t70) cc_final: 0.7569 (t0) REVERT: C 102 ARG cc_start: 0.8488 (mmt180) cc_final: 0.8109 (mmt90) REVERT: C 290 ASP cc_start: 0.8765 (t0) cc_final: 0.8546 (t0) REVERT: C 606 ASN cc_start: 0.7620 (m110) cc_final: 0.7353 (t0) REVERT: C 613 GLN cc_start: 0.8316 (mt0) cc_final: 0.7120 (tt0) REVERT: C 636 TYR cc_start: 0.7808 (m-10) cc_final: 0.7569 (m-10) REVERT: C 702 VAL cc_start: 0.8114 (p) cc_final: 0.7862 (m) REVERT: C 820 PHE cc_start: 0.8226 (t80) cc_final: 0.7329 (m-80) REVERT: C 1104 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7767 (mpt180) REVERT: B 62 VAL cc_start: 0.7784 (t) cc_final: 0.7569 (t) REVERT: B 66 HIS cc_start: 0.6325 (m90) cc_final: 0.6052 (m170) REVERT: B 115 GLN cc_start: 0.8889 (mt0) cc_final: 0.8570 (mt0) REVERT: B 567 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7696 (mmm-85) REVERT: B 606 ASN cc_start: 0.8006 (t0) cc_final: 0.7798 (t0) REVERT: B 613 GLN cc_start: 0.8771 (mt0) cc_final: 0.8517 (mt0) REVERT: B 787 LYS cc_start: 0.8598 (mttm) cc_final: 0.8262 (mttm) REVERT: B 999 GLN cc_start: 0.8225 (tt0) cc_final: 0.7700 (pt0) REVERT: B 1035 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8268 (mmtm) REVERT: B 1133 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7528 (p) REVERT: A 207 HIS cc_start: 0.8025 (t-90) cc_final: 0.7499 (m-70) REVERT: A 309 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 613 GLN cc_start: 0.8331 (mp10) cc_final: 0.7465 (tt0) REVERT: A 699 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 1070 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7215 (mmtp) REVERT: A 1115 ASP cc_start: 0.8056 (p0) cc_final: 0.7832 (p0) outliers start: 96 outliers final: 56 residues processed: 323 average time/residue: 0.1550 time to fit residues: 82.0367 Evaluate side-chains 281 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 237 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 307 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN C 898 GLN A 81 ASN A 487 ASN A 606 ASN A 898 GLN A 917 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117025 restraints weight = 30228.067| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.51 r_work: 0.3020 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25417 Z= 0.182 Angle : 0.668 20.120 34566 Z= 0.344 Chirality : 0.048 0.325 3974 Planarity : 0.005 0.069 4419 Dihedral : 7.532 79.681 3421 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.03 % Allowed : 17.21 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3063 helix: -0.18 (0.20), residues: 667 sheet: -0.59 (0.20), residues: 685 loop : -2.76 (0.12), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.027 0.002 TYR A 37 PHE 0.016 0.002 PHE B 201 TRP 0.012 0.002 TRP A 353 HIS 0.004 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (25379) covalent geometry : angle 0.64603 / 0.34 (34483) SS BOND : bond 0.00439 / 0.26 ( 31) SS BOND : angle 1.39912 / 0.88 ( 62) hydrogen bonds : bond 0.05492 / 3.61 ( 857) hydrogen bonds : angle 5.20590 / 3.67 ( 2313) link_BETA1-4 : bond 0.00674 / 0.35 ( 1) link_BETA1-4 : angle 2.77905 / 1.37 ( 3) link_NAG-ASN : bond 0.00510 / 0.39 ( 6) link_NAG-ASN : angle 6.96790 / 4.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 232 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8221 (t70) cc_final: 0.7403 (t0) REVERT: C 102 ARG cc_start: 0.8577 (mmt180) cc_final: 0.8232 (mmt90) REVERT: C 290 ASP cc_start: 0.8889 (t0) cc_final: 0.8621 (t0) REVERT: C 606 ASN cc_start: 0.7663 (m110) cc_final: 0.7395 (t0) REVERT: C 820 PHE cc_start: 0.8356 (t80) cc_final: 0.7348 (m-80) REVERT: C 983 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8270 (tmtm) REVERT: B 62 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7808 (t) REVERT: B 158 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7136 (mtt180) REVERT: B 606 ASN cc_start: 0.8126 (t0) cc_final: 0.7727 (t0) REVERT: B 613 GLN cc_start: 0.8671 (mt0) cc_final: 0.8438 (mt0) REVERT: B 661 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 787 LYS cc_start: 0.8629 (mttm) cc_final: 0.8270 (mttm) REVERT: A 207 HIS cc_start: 0.8068 (t-90) cc_final: 0.7559 (m-70) REVERT: A 699 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: A 932 GLN cc_start: 0.8012 (tt0) cc_final: 0.7608 (tt0) REVERT: A 1070 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7387 (mmtp) outliers start: 109 outliers final: 72 residues processed: 316 average time/residue: 0.1534 time to fit residues: 78.6151 Evaluate side-chains 300 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 224 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN C 850 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS B1122 ASN A 69 HIS A 81 ASN A 898 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122807 restraints weight = 29869.219| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.41 r_work: 0.3107 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25417 Z= 0.138 Angle : 0.602 17.585 34566 Z= 0.313 Chirality : 0.045 0.238 3974 Planarity : 0.004 0.067 4419 Dihedral : 7.149 76.193 3413 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.58 % Allowed : 18.25 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.14), residues: 3063 helix: 0.18 (0.20), residues: 659 sheet: -0.35 (0.20), residues: 683 loop : -2.57 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1104 TYR 0.023 0.001 TYR A 37 PHE 0.015 0.001 PHE A 377 TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (25379) covalent geometry : angle 0.58525 / 0.31 (34483) SS BOND : bond 0.00327 / 0.20 ( 31) SS BOND : angle 1.12868 / 0.69 ( 62) hydrogen bonds : bond 0.04730 / 3.13 ( 857) hydrogen bonds : angle 5.03548 / 3.54 ( 2313) link_BETA1-4 : bond 0.00584 / 0.31 ( 1) link_BETA1-4 : angle 2.46869 / 1.20 ( 3) link_NAG-ASN : bond 0.00548 / 0.44 ( 6) link_NAG-ASN : angle 5.85419 / 3.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 235 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: C 32 PHE cc_start: 0.7307 (m-80) cc_final: 0.7024 (m-80) REVERT: C 88 ASP cc_start: 0.8204 (t70) cc_final: 0.7339 (t0) REVERT: C 290 ASP cc_start: 0.8882 (t0) cc_final: 0.8613 (t0) REVERT: C 568 ASP cc_start: 0.7634 (t0) cc_final: 0.7281 (t0) REVERT: C 606 ASN cc_start: 0.7662 (m110) cc_final: 0.7449 (t0) REVERT: C 613 GLN cc_start: 0.8320 (mt0) cc_final: 0.7224 (tt0) REVERT: C 820 PHE cc_start: 0.8318 (t80) cc_final: 0.7336 (m-80) REVERT: C 983 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8314 (tmtm) REVERT: B 62 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7794 (t) REVERT: B 158 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7175 (mtt180) REVERT: B 606 ASN cc_start: 0.8194 (t0) cc_final: 0.7750 (t0) REVERT: B 613 GLN cc_start: 0.8720 (mt0) cc_final: 0.8439 (mt0) REVERT: B 787 LYS cc_start: 0.8619 (mttm) cc_final: 0.8247 (mttm) REVERT: B 891 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 999 GLN cc_start: 0.8350 (tt0) cc_final: 0.8114 (tp-100) REVERT: B 1035 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8321 (mmtp) REVERT: B 1042 LYS cc_start: 0.8674 (tmtm) cc_final: 0.8155 (mmtt) REVERT: A 207 HIS cc_start: 0.8082 (t-90) cc_final: 0.7584 (m-70) REVERT: A 309 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: A 613 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: A 675 GLN cc_start: 0.7115 (tt0) cc_final: 0.6863 (tt0) REVERT: A 699 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 776 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: A 932 GLN cc_start: 0.7966 (tt0) cc_final: 0.7553 (tt0) REVERT: A 947 ASP cc_start: 0.8429 (m-30) cc_final: 0.8197 (m-30) REVERT: A 1070 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7484 (mmtp) outliers start: 97 outliers final: 73 residues processed: 309 average time/residue: 0.1574 time to fit residues: 78.8157 Evaluate side-chains 308 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 227 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 GLN C 798 ASN C 898 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121815 restraints weight = 30320.719| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.61 r_work: 0.3061 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25417 Z= 0.095 Angle : 0.530 15.219 34566 Z= 0.275 Chirality : 0.044 0.296 3974 Planarity : 0.004 0.059 4419 Dihedral : 6.763 70.461 3412 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.07 % Allowed : 18.91 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3063 helix: 0.63 (0.21), residues: 659 sheet: -0.13 (0.20), residues: 680 loop : -2.34 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1104 TYR 0.020 0.001 TYR C 265 PHE 0.018 0.001 PHE A 377 TRP 0.013 0.001 TRP B 64 HIS 0.002 0.000 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (25379) covalent geometry : angle 0.51853 / 0.27 (34483) SS BOND : bond 0.00403 / 0.16 ( 31) SS BOND : angle 0.78247 / 0.49 ( 62) hydrogen bonds : bond 0.03636 / 2.40 ( 857) hydrogen bonds : angle 4.82562 / 3.40 ( 2313) link_BETA1-4 : bond 0.00563 / 0.30 ( 1) link_BETA1-4 : angle 1.96553 / 0.97 ( 3) link_NAG-ASN : bond 0.00236 / 0.14 ( 6) link_NAG-ASN : angle 4.58260 / 2.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 1.083 Fit side-chains REVERT: C 32 PHE cc_start: 0.7146 (m-80) cc_final: 0.6939 (m-80) REVERT: C 88 ASP cc_start: 0.8166 (t70) cc_final: 0.7524 (t0) REVERT: C 102 ARG cc_start: 0.8495 (mmt180) cc_final: 0.8114 (mmt90) REVERT: C 290 ASP cc_start: 0.8844 (t0) cc_final: 0.8570 (t0) REVERT: C 613 GLN cc_start: 0.8262 (mt0) cc_final: 0.7193 (tt0) REVERT: C 820 PHE cc_start: 0.8328 (t80) cc_final: 0.7311 (m-80) REVERT: C 1104 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7865 (mpt180) REVERT: B 158 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6938 (mtt180) REVERT: B 271 GLN cc_start: 0.8317 (pt0) cc_final: 0.8007 (mt0) REVERT: B 445 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6290 (t) REVERT: B 567 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7659 (mmm-85) REVERT: B 606 ASN cc_start: 0.8132 (t0) cc_final: 0.7891 (t0) REVERT: B 613 GLN cc_start: 0.8582 (mt0) cc_final: 0.8332 (mt0) REVERT: B 787 LYS cc_start: 0.8670 (mttm) cc_final: 0.8410 (mttm) REVERT: B 891 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 999 GLN cc_start: 0.8303 (tt0) cc_final: 0.8038 (tp-100) REVERT: B 1035 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8240 (mmtm) REVERT: A 207 HIS cc_start: 0.7970 (t-90) cc_final: 0.7388 (m170) REVERT: A 244 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5199 (mt) REVERT: A 309 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 500 THR cc_start: 0.8191 (p) cc_final: 0.7836 (t) REVERT: A 675 GLN cc_start: 0.6989 (tt0) cc_final: 0.6718 (tt0) REVERT: A 932 GLN cc_start: 0.7832 (tt0) cc_final: 0.7443 (tt0) REVERT: A 947 ASP cc_start: 0.8415 (m-30) cc_final: 0.8154 (m-30) REVERT: A 1070 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7299 (mmtp) REVERT: A 1125 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6465 (p) outliers start: 83 outliers final: 54 residues processed: 313 average time/residue: 0.1734 time to fit residues: 87.0827 Evaluate side-chains 290 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 0.5980 chunk 193 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 228 optimal weight: 5.9990 chunk 233 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN C 898 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN A 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115129 restraints weight = 30643.669| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.63 r_work: 0.3011 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25417 Z= 0.133 Angle : 0.567 8.658 34566 Z= 0.297 Chirality : 0.045 0.216 3974 Planarity : 0.004 0.066 4419 Dihedral : 6.724 66.154 3407 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.55 % Allowed : 18.95 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3063 helix: 0.53 (0.21), residues: 666 sheet: -0.06 (0.20), residues: 679 loop : -2.30 (0.13), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1104 TYR 0.025 0.001 TYR B 37 PHE 0.017 0.001 PHE A 377 TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (25379) covalent geometry : angle 0.56177 / 0.30 (34483) SS BOND : bond 0.00327 / 0.20 ( 31) SS BOND : angle 1.04752 / 0.66 ( 62) hydrogen bonds : bond 0.04484 / 2.96 ( 857) hydrogen bonds : angle 4.87559 / 3.43 ( 2313) link_BETA1-4 : bond 0.00452 / 0.24 ( 1) link_BETA1-4 : angle 2.12209 / 1.03 ( 3) link_NAG-ASN : bond 0.00200 / 0.13 ( 6) link_NAG-ASN : angle 2.96802 / 1.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 230 time to evaluate : 1.025 Fit side-chains REVERT: C 32 PHE cc_start: 0.7205 (m-80) cc_final: 0.6992 (m-80) REVERT: C 88 ASP cc_start: 0.8280 (t70) cc_final: 0.7529 (t0) REVERT: C 102 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8114 (mmt90) REVERT: C 290 ASP cc_start: 0.8907 (t0) cc_final: 0.8634 (t0) REVERT: C 613 GLN cc_start: 0.8325 (mt0) cc_final: 0.7174 (tt0) REVERT: C 820 PHE cc_start: 0.8331 (t80) cc_final: 0.7292 (m-80) REVERT: B 129 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7624 (mtmt) REVERT: B 158 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6912 (mtt180) REVERT: B 445 VAL cc_start: 0.6409 (OUTLIER) cc_final: 0.6177 (t) REVERT: B 606 ASN cc_start: 0.8142 (t0) cc_final: 0.7873 (t0) REVERT: B 661 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: B 787 LYS cc_start: 0.8644 (mttm) cc_final: 0.8409 (mttm) REVERT: B 999 GLN cc_start: 0.8387 (tt0) cc_final: 0.8157 (tp-100) REVERT: B 1035 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8270 (mmtt) REVERT: A 207 HIS cc_start: 0.8032 (t-90) cc_final: 0.7449 (m170) REVERT: A 244 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5176 (mt) REVERT: A 613 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: A 675 GLN cc_start: 0.7235 (tt0) cc_final: 0.6928 (tt0) REVERT: A 776 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8193 (tp40) REVERT: A 947 ASP cc_start: 0.8444 (m-30) cc_final: 0.8157 (m-30) REVERT: A 1070 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7334 (mmtp) REVERT: A 1125 VAL cc_start: 0.6963 (OUTLIER) cc_final: 0.6551 (p) outliers start: 96 outliers final: 76 residues processed: 303 average time/residue: 0.1679 time to fit residues: 82.4451 Evaluate side-chains 308 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 224 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 58 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN B 474 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121643 restraints weight = 30114.598| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.48 r_work: 0.3029 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25417 Z= 0.122 Angle : 0.553 8.536 34566 Z= 0.290 Chirality : 0.044 0.193 3974 Planarity : 0.004 0.069 4419 Dihedral : 6.645 62.126 3405 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.66 % Allowed : 19.06 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 3063 helix: 0.60 (0.21), residues: 666 sheet: 0.02 (0.20), residues: 675 loop : -2.23 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.022 0.001 TYR A 37 PHE 0.015 0.001 PHE A 377 TRP 0.012 0.001 TRP B 64 HIS 0.002 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (25379) covalent geometry : angle 0.54776 / 0.29 (34483) SS BOND : bond 0.00316 / 0.20 ( 31) SS BOND : angle 1.01479 / 0.63 ( 62) hydrogen bonds : bond 0.04331 / 2.86 ( 857) hydrogen bonds : angle 4.84611 / 3.41 ( 2313) link_BETA1-4 : bond 0.00515 / 0.27 ( 1) link_BETA1-4 : angle 2.13726 / 1.05 ( 3) link_NAG-ASN : bond 0.00161 / 0.08 ( 6) link_NAG-ASN : angle 2.69018 / 1.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 1.166 Fit side-chains REVERT: C 32 PHE cc_start: 0.7218 (m-80) cc_final: 0.7016 (m-80) REVERT: C 88 ASP cc_start: 0.8254 (t70) cc_final: 0.7505 (t0) REVERT: C 290 ASP cc_start: 0.8900 (t0) cc_final: 0.8628 (t0) REVERT: C 613 GLN cc_start: 0.8316 (mt0) cc_final: 0.7233 (tt0) REVERT: C 820 PHE cc_start: 0.8348 (t80) cc_final: 0.7312 (m-80) REVERT: B 129 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: B 158 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6980 (mtt180) REVERT: B 445 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6521 (t) REVERT: B 606 ASN cc_start: 0.8132 (t0) cc_final: 0.7855 (t0) REVERT: B 787 LYS cc_start: 0.8680 (mttm) cc_final: 0.8451 (mttm) REVERT: B 1035 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8278 (mmtt) REVERT: A 207 HIS cc_start: 0.8029 (t-90) cc_final: 0.7459 (m170) REVERT: A 244 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5212 (mt) REVERT: A 500 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7862 (t) REVERT: A 613 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: A 675 GLN cc_start: 0.7260 (tt0) cc_final: 0.6987 (tt0) REVERT: A 947 ASP cc_start: 0.8466 (m-30) cc_final: 0.8189 (m-30) REVERT: A 1070 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7398 (mmtp) REVERT: A 1125 VAL cc_start: 0.6979 (OUTLIER) cc_final: 0.6560 (p) outliers start: 99 outliers final: 80 residues processed: 311 average time/residue: 0.1647 time to fit residues: 82.7555 Evaluate side-chains 314 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 240 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN C 898 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118820 restraints weight = 30502.972| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.63 r_work: 0.3085 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25417 Z= 0.089 Angle : 0.500 7.786 34566 Z= 0.262 Chirality : 0.043 0.162 3974 Planarity : 0.004 0.064 4419 Dihedral : 6.275 59.202 3405 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.07 % Allowed : 19.50 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 3063 helix: 0.89 (0.21), residues: 674 sheet: 0.16 (0.20), residues: 678 loop : -2.12 (0.13), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.019 0.001 TYR C 265 PHE 0.016 0.001 PHE C 797 TRP 0.013 0.001 TRP B 64 HIS 0.002 0.000 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (25379) covalent geometry : angle 0.49618 / 0.26 (34483) SS BOND : bond 0.00209 / 0.12 ( 31) SS BOND : angle 0.83069 / 0.49 ( 62) hydrogen bonds : bond 0.03411 / 2.25 ( 857) hydrogen bonds : angle 4.64118 / 3.26 ( 2313) link_BETA1-4 : bond 0.00327 / 0.17 ( 1) link_BETA1-4 : angle 1.68985 / 0.84 ( 3) link_NAG-ASN : bond 0.00191 / 0.09 ( 6) link_NAG-ASN : angle 2.28464 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 247 time to evaluate : 0.821 Fit side-chains REVERT: C 88 ASP cc_start: 0.8164 (t70) cc_final: 0.7468 (t0) REVERT: C 102 ARG cc_start: 0.8417 (mmt180) cc_final: 0.8092 (mmt90) REVERT: C 290 ASP cc_start: 0.8853 (t0) cc_final: 0.8610 (t0) REVERT: C 474 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6718 (mt0) REVERT: C 487 ASN cc_start: 0.6431 (m-40) cc_final: 0.6157 (t0) REVERT: C 568 ASP cc_start: 0.7564 (t0) cc_final: 0.7243 (t0) REVERT: C 571 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8116 (t0) REVERT: C 613 GLN cc_start: 0.8160 (mt0) cc_final: 0.7129 (tt0) REVERT: C 756 PHE cc_start: 0.7729 (m-80) cc_final: 0.7521 (m-80) REVERT: C 798 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8449 (m-40) REVERT: C 820 PHE cc_start: 0.8291 (t80) cc_final: 0.7263 (m-80) REVERT: C 1047 MET cc_start: 0.8757 (ptp) cc_final: 0.8520 (ptm) REVERT: B 158 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6924 (mtt180) REVERT: B 271 GLN cc_start: 0.8264 (pt0) cc_final: 0.7914 (mt0) REVERT: B 343 ASN cc_start: 0.7659 (t0) cc_final: 0.7406 (t0) REVERT: B 567 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7458 (mmm-85) REVERT: B 606 ASN cc_start: 0.8034 (t0) cc_final: 0.7768 (t0) REVERT: B 787 LYS cc_start: 0.8649 (mttm) cc_final: 0.8426 (mttm) REVERT: B 1035 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8255 (mmtt) REVERT: B 1132 ASN cc_start: 0.7110 (t0) cc_final: 0.6896 (t0) REVERT: A 207 HIS cc_start: 0.7928 (t-90) cc_final: 0.7296 (m170) REVERT: A 244 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5178 (mt) REVERT: A 309 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 500 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7856 (t) REVERT: A 613 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 675 GLN cc_start: 0.7130 (tt0) cc_final: 0.6866 (tt0) REVERT: A 947 ASP cc_start: 0.8397 (m-30) cc_final: 0.8145 (m-30) REVERT: A 1070 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7331 (mmtp) REVERT: A 1125 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6502 (p) outliers start: 83 outliers final: 59 residues processed: 311 average time/residue: 0.1631 time to fit residues: 81.7633 Evaluate side-chains 298 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 231 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 224 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 119 optimal weight: 0.0370 chunk 294 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN C 898 GLN B 66 HIS ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 115 GLN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113988 restraints weight = 30391.233| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.53 r_work: 0.2969 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25417 Z= 0.256 Angle : 0.704 9.449 34566 Z= 0.369 Chirality : 0.050 0.268 3974 Planarity : 0.005 0.079 4419 Dihedral : 6.837 58.366 3397 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.66 % Allowed : 18.99 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3063 helix: 0.21 (0.20), residues: 672 sheet: 0.01 (0.20), residues: 673 loop : -2.27 (0.13), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.042 0.002 TYR B 37 PHE 0.022 0.002 PHE C 797 TRP 0.017 0.002 TRP B 64 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (25379) covalent geometry : angle 0.69716 / 0.37 (34483) SS BOND : bond 0.00627 / 0.37 ( 31) SS BOND : angle 1.70736 / 1.05 ( 62) hydrogen bonds : bond 0.06174 / 4.08 ( 857) hydrogen bonds : angle 5.17547 / 3.65 ( 2313) link_BETA1-4 : bond 0.00507 / 0.27 ( 1) link_BETA1-4 : angle 2.86375 / 1.40 ( 3) link_NAG-ASN : bond 0.00228 / 0.08 ( 6) link_NAG-ASN : angle 2.99673 / 1.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 1.024 Fit side-chains REVERT: C 88 ASP cc_start: 0.8316 (t70) cc_final: 0.7486 (t0) REVERT: C 290 ASP cc_start: 0.9045 (t0) cc_final: 0.8790 (t0) REVERT: C 585 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8509 (mt) REVERT: C 820 PHE cc_start: 0.8378 (t80) cc_final: 0.7260 (m-80) REVERT: B 158 ARG cc_start: 0.7317 (mtt180) cc_final: 0.7024 (mtt180) REVERT: B 606 ASN cc_start: 0.8147 (t0) cc_final: 0.7876 (t0) REVERT: B 661 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: B 787 LYS cc_start: 0.8698 (mttm) cc_final: 0.8431 (mttm) REVERT: B 1089 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 207 HIS cc_start: 0.8049 (t-90) cc_final: 0.7529 (m170) REVERT: A 309 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 613 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 675 GLN cc_start: 0.7516 (tt0) cc_final: 0.7239 (tt0) REVERT: A 776 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8210 (tp40) REVERT: A 1070 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7482 (mmtp) REVERT: A 1125 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6563 (p) outliers start: 99 outliers final: 76 residues processed: 309 average time/residue: 0.1646 time to fit residues: 82.0454 Evaluate side-chains 307 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 153 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 798 ASN B 613 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS A 81 ASN A 87 ASN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.115340 restraints weight = 30523.776| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.65 r_work: 0.3017 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25417 Z= 0.118 Angle : 0.552 10.029 34566 Z= 0.291 Chirality : 0.045 0.203 3974 Planarity : 0.004 0.069 4419 Dihedral : 6.415 57.357 3397 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.62 % Allowed : 19.95 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3063 helix: 0.63 (0.21), residues: 665 sheet: 0.08 (0.20), residues: 679 loop : -2.16 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.021 0.001 TYR A 37 PHE 0.016 0.001 PHE A 820 TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (25379) covalent geometry : angle 0.54804 / 0.29 (34483) SS BOND : bond 0.00276 / 0.17 ( 31) SS BOND : angle 1.02103 / 0.62 ( 62) hydrogen bonds : bond 0.04249 / 2.81 ( 857) hydrogen bonds : angle 4.85591 / 3.43 ( 2313) link_BETA1-4 : bond 0.00593 / 0.31 ( 1) link_BETA1-4 : angle 2.14922 / 1.06 ( 3) link_NAG-ASN : bond 0.00184 / 0.09 ( 6) link_NAG-ASN : angle 2.50484 / 1.70 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 0.910 Fit side-chains REVERT: C 88 ASP cc_start: 0.8279 (t70) cc_final: 0.7487 (t0) REVERT: C 102 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8173 (mmt90) REVERT: C 290 ASP cc_start: 0.8991 (t0) cc_final: 0.8734 (t0) REVERT: C 474 GLN cc_start: 0.7551 (tm-30) cc_final: 0.6772 (mt0) REVERT: C 568 ASP cc_start: 0.7695 (t0) cc_final: 0.7396 (t0) REVERT: C 613 GLN cc_start: 0.8274 (mt0) cc_final: 0.7145 (tt0) REVERT: C 756 PHE cc_start: 0.7943 (m-80) cc_final: 0.7716 (m-80) REVERT: C 820 PHE cc_start: 0.8321 (t80) cc_final: 0.7253 (m-80) REVERT: B 158 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6919 (mtt180) REVERT: B 567 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7685 (mmm-85) REVERT: B 606 ASN cc_start: 0.8123 (t0) cc_final: 0.7843 (t0) REVERT: B 613 GLN cc_start: 0.8868 (mt0) cc_final: 0.8499 (mt0) REVERT: B 661 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: B 787 LYS cc_start: 0.8684 (mttm) cc_final: 0.8426 (mttm) REVERT: B 914 TYR cc_start: 0.8081 (m-80) cc_final: 0.7657 (m-80) REVERT: B 1035 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8270 (mmtt) REVERT: B 1089 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 207 HIS cc_start: 0.8020 (t-90) cc_final: 0.7443 (m170) REVERT: A 309 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 500 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7881 (t) REVERT: A 613 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: A 675 GLN cc_start: 0.7365 (tt0) cc_final: 0.7088 (tt0) REVERT: A 1070 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7362 (mmtp) REVERT: A 1125 VAL cc_start: 0.6988 (OUTLIER) cc_final: 0.6599 (p) outliers start: 71 outliers final: 60 residues processed: 281 average time/residue: 0.1725 time to fit residues: 77.7259 Evaluate side-chains 287 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 86 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 144 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.143103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116185 restraints weight = 30555.622| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.69 r_work: 0.3032 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25417 Z= 0.114 Angle : 0.543 9.210 34566 Z= 0.286 Chirality : 0.044 0.207 3974 Planarity : 0.004 0.068 4419 Dihedral : 6.239 56.797 3397 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.77 % Allowed : 19.95 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 3063 helix: 0.72 (0.21), residues: 671 sheet: 0.17 (0.20), residues: 673 loop : -2.12 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.020 0.001 TYR A 37 PHE 0.016 0.001 PHE A 820 TRP 0.012 0.001 TRP B 64 HIS 0.002 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (25379) covalent geometry : angle 0.53921 / 0.29 (34483) SS BOND : bond 0.00267 / 0.16 ( 31) SS BOND : angle 0.98958 / 0.61 ( 62) hydrogen bonds : bond 0.04146 / 2.74 ( 857) hydrogen bonds : angle 4.79034 / 3.38 ( 2313) link_BETA1-4 : bond 0.00504 / 0.27 ( 1) link_BETA1-4 : angle 2.05549 / 1.01 ( 3) link_NAG-ASN : bond 0.00155 / 0.08 ( 6) link_NAG-ASN : angle 2.39914 / 1.63 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6927.60 seconds wall clock time: 119 minutes 8.89 seconds (7148.89 seconds total)